Requirements
Genecoder molecular biology software is platform independent and only requires JavaTM 1.5 or later.
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GeneCoder Frequently Asked Questions
Technique:
1) What is the purpose of a Region?
2) How do I change my enzyme Preferences?
3) How can I find an Open Reading Frame?
4) Can I check the sequence traces of a clone?
5) How do I design siRNA oligos?
6) How can I create a comprehensive plasmid map?
General:
4) Genecoder keeps creating two files, CommonSeq.pref and RELibrary.pref. Why?
5) Genecoder writes its own files. Is the format publicly available?
1) What is the purpose of a Region? Regions can be used to save important sequence features, such as an open reading frame, promoter, polylinker, etc...Regions are important in the creation of comprehensive maps, where a polylinker region must be defined to create particular plasmid maps and important in the common sequence search tool, where identified sequences are added as regions.
2) How do I change my enzyme Preferences? Enzyme preferences and enzyme data can be changed using the Enzyme menu. To view a small selection of restriction enzymes, use the Enzyme Preference window to select the enzymes of interest. Enzymes can be added and/or modified and all changes are saved to the the RELibrary.pref file.
3) How can I find an Open Reading Frame (ORF)? Open reading frames can be found in a number of ways. First, using the Analyze->Find ORF (Command-R) menu will allow you to iterate through the sequence to look for possible ORF's. Alternatively, using the Sequence->Translation menu one can find ORF's via one phase translation, three phase translation, and/or using the graphical interface. A new region can be added or a new protein file created by Double clicking an ORF in the graphical user interface.
4) Can I check the sequence traces of a clone? Yes. Go to Analyze->Alignments->Continunous Align->Compare. Select a reference sequence and input sequences to align. Genecoder will perform alignments as well as report potential errors in the alignment. A minimum homology is necessary to complete the alignment - GeneCoder will report any sequences that could not be aligned. If you wish to analyze a potential sequence error in a trace chromatogram, reveal the location of the error in the alignment by clicking the error in the table. Double clicking the nucleotide in the sequence alignment window will show and highlight the location in the trace.
5) How do I design siRNA oligos? To design target oligos for siRNA, open the DNA sequence to target. Select Analyze->Oligo Tools->Design siRNA Oligo(s). A new window forms with potential siRNA oligos ordered by score. Score is an arbitratrary and relative value generated by the rules for penalties and awards based upon our current understanding of siRNA. If you wish to search for potential off-target effect, click on the NCBI/Entrez tab, a new BLAST window will open with default BLAST parameters to search for short and nearly identical sequences - BE SURE TO SELECT THE APPROPRIATE DATABASE TO BLAST. Given the ever-expanding number of different targeting plasmids and protocols used for shRNA, Genecoder does not currently support the creation of oligos with shRNA loops and/or sticky ends.
6) How can I create a comprehensive plasmid map? Comprehensive maps can be created via the Analyze->Plasmid Maps Menu. To generate a map, common sequences (such as AMP resistance, promoters, etc...) can be searched for using the Analyze->Common Sequences menu item - Genecoder will search for sequences and asign a new region for each sequence found. To create particular plasmid maps, a polylinker must manually be defined as a region. To generate the map, go to Analyze->Plasmid Maps->Create Comprehensive Map. Select preferences and reading frame (if necessary), then choose your map. Maps can be saved and reopened later - maps are saved as a jpg file and can be re-opened in any standard image editor.
General:
1) Is Genecoder Open Source? Genecoder was originally written in C and C++, then ported to Java for multiplatform compatability. At this time, source code for any version of GeneCoder is not publicly available and all code and executables are © 2005-2008 Greg Cope.
2) Why is GeneCoder free? Genecoder was originally written by a Biology Graduate Student frustrated with the current molecular biology software. Keyservers and price tags of the software at the time promoted the creation of the Genecoder project. However, the development of GeneCoder as well as the development and hosting of this website are not free.
3) How can I contribute? Genecoder is free software, yet its development is not. If you are a software engineer or designer wishing to contribute your knowledge and expertise, please contact Greg Cope. If you wish to otherwise contribute, you are encouraged to make a donation.
4) Genecoder keeps creating two files, CommonSeq.pref and RELibrary.pref. Why? These two files are the accompanying database files for a Restriction Enzyme Library and Common Sequence library. The files allow users to add and/or modify each database. If Genecoder cannot find these files it will recreate them with default values. It is recommended that Genecoder remain in its own folder/directory to organize these accompanying files with the program.
5) Genecoder writes its own files. Is the format publicly available? Files opened as Genecoder format can be exported as FASTA and/or plain text for use in other tools. If you wish to 'hack' the file format, please contact Greg Cope for more information on the file format structure.